Package org.cipres.treebase.domain.tree

Examples of org.cipres.treebase.domain.tree.TreeBlock

96
97
98
99
100
101
102
103
104
105
106
                Map<String,String> nexusMap = t.getStudy().getNexusFiles();
                String nexusFile = nexusMap.remove(nexusFileName);
                s.getNexusFiles().put(nexusFileName, nexusFile);
                t.setStudy(s);
              }
              TreeBlock tb = t.getTreeBlock();
              if (tb == null) {
                System.err.println("  No tree block!");
              } else if (! tbs.contains(tb)) {
                Submission oldSub = sh.findByTreeBlock(tb);
                if (oldSub != null) {
View Full Code Here
56
57
58
59
60
61
62
63
64
65
66
67
    }   
   
    // Trees
    NexmlTreeBlockReader ntbc = new NexmlTreeBlockReader(pStudy,getTaxonLabelHome(),document);
    for ( org.nexml.model.TreeBlock xmlTreeBlock : document.getTreeBlockList() ) {
      TreeBlock tbTreeBlock = ntbc.fromXmlToTreeBase(xmlTreeBlock);
      for ( PhyloTree phyloTree : tbTreeBlock.getTreeList() ) {
        phyloTree.setNexusFileName(pFile.getName());
      }
      pDataSet.getTreeBlocks().add(tbTreeBlock);
    } 
   
View Full Code Here
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
      // bi-directional relationships:
      // * delete treeblock -> tree
      // * delete submission-> tree
      // * delete analyzedData -> tree
      TreeBlock block = pTree.getTreeBlock();
      if (block != null) {
        block.removePhyloTree(pTree);

        if (block.isEmpty()) {
          //TaxonLabelSet tSet=block.getTaxonLabelSet();
          deleteTreeBlock(block);
          //getTaxonLabelHome().clean(tSet);
        }
      }
View Full Code Here
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
   * @return
   */
  public TreeBlock fromXmlToTreeBase(org.nexml.model.TreeBlock xmlTreeBlock) {
    OTUs xmlOTUs = xmlTreeBlock.getOTUs();
    Long tbTaxonLabelSetId = readTreeBaseID(xmlOTUs);
    TreeBlock tbTreeBlock = new TreeBlock();
    tbTreeBlock.setTitle(xmlTreeBlock.getLabel());
    if ( null != tbTaxonLabelSetId ) {
      TaxonLabelSet tbTaxonLabelSet = getTaxonLabelHome()
        .findPersistedObjectByID(TaxonLabelSet.class, tbTaxonLabelSetId);
      tbTreeBlock.setTaxonLabelSet(tbTaxonLabelSet);
    }
    Iterator<Network<?>> xmlNetworkIterator = xmlTreeBlock.iterator();
    while ( xmlNetworkIterator.hasNext() ) {
      Network<?> xmlNetwork = xmlNetworkIterator.next();
      if ( xmlNetwork instanceof Tree ) {
        PhyloTree tbPhyloTree = fromXmlToTreeBase((Tree<?>) xmlNetwork);
        tbPhyloTree.setStudy(getStudy());
        tbTreeBlock.addPhyloTree(tbPhyloTree);
      }       
    }   
    return tbTreeBlock;
  }
View Full Code Here
32
33
34
35
36
37
38
39
40
41
42
      study = tree.getStudy();
    }
    if (pRequest.getParameter("treeblockid") != null) {
      String treeBlockId = pRequest.getParameter("treeblockid");
      Long value = Long.parseLong(treeBlockId);
      TreeBlock treeBlock = getPhyloTreeHome().findTreeBlockById(value);
      study = getSubmissionHome().findByTreeBlock(treeBlock).getStudy();
    }
    if ( ControllerUtil.isReviewerAccessGranted(pRequest) || ( study != null && study.isPublished() ) ) {
      return super.handleRequest(pRequest, pResponse);
    }
View Full Code Here
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
      return new AGenericList<Collection<PhyloTree>>(new ArrayList<PhyloTree>());
    }

    Long value = Long.parseLong(TBID);

    TreeBlock treeblock = getPhyloTreeHome().findTreeBlockById(value);
    // It can happen that the TBID is saved but the tree-block has been deleted
    // Or the only tree in the block has been removed.
    if (treeblock != null) {

      Long submission_id = getSubmissionHome().findByTreeBlock(treeblock).getId();
      TBPermission perm2 = getSubmissionService().getPermission(
        request.getRemoteUser(),
        submission_id);
      if (perm2 == TBPermission.WRITE || perm2 == TBPermission.SUBMITTED_WRITE) {
        LOGGER.info("setAuthorizationChecked(true)");
        setAuthorizationChecked(true);
        Collection<PhyloTree> phyloTreeList = treeblock.getTreeList();
        ControllerUtil.setTreeBlockId(TBID, request);
        checkAnalyzed(phyloTreeList,ControllerUtil.findStudy(request, mStudyService));
        // This ID has to be saved for success/cancel view.
        return new AGenericList<Collection<PhyloTree>>(phyloTreeList);
      } else {
View Full Code Here
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
    return "TB";
  }

  @Override
  protected String getFileContent(long blockid, HttpServletRequest request) {
    TreeBlock treeBlock = getPhyloTreeHome().findTreeBlockById(blockid);   
    if ( getFormat(request) == FORMAT_NEXML || getFormat(request) == FORMAT_RDF ) {
      NexusDataSet nexusDataSet = new NexusDataSet();
      nexusDataSet.getTaxonLabelSets().add(treeBlock.getTaxonLabelSet());
      nexusDataSet.getTreeBlocks().add(treeBlock);
      return getNexmlService().serialize(nexusDataSet,getDefaultProperties(request));
    }
    /*else if ( getFormat(request) == FORMAT_RDF ) {
      NexusDataSet nexusDataSet = new NexusDataSet();
      nexusDataSet.getTaxonLabelSets().add(treeBlock.getTaxonLabelSet());
      nexusDataSet.getTreeBlocks().add(treeBlock);     
      return getRdfaService().serialize(nexusDataSet,getDefaultProperties(request));     
    }*/   
    else {
      StringBuilder bldr = new StringBuilder("#NEXUS\n\n");
      treeBlock.generateAFileDynamically(bldr);
      return bldr.toString();
    }
  }
View Full Code Here
117
118
119
120
121
122
123
124
125
    }
  }

  @Override
  protected Study getStudy(long objectId, HttpServletRequest request) {
    TreeBlock treeBlock = getPhyloTreeHome().findTreeBlockById(objectId);
    Submission submission = getSubmissionHome().findByTreeBlock(treeBlock);
    return submission.getStudy();   
  }
View Full Code Here
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
    if (pRequest.getParameter("treeblockid") != null) {

      String TBID = pRequest.getParameter("treeblockid");
      Long value = Long.parseLong(TBID);

      TreeBlock TB = getPhyloTreeHome().findTreeBlockById(value);

      if (TB.getTitle().startsWith("Tree")) {
        newickStringName = TB.getTitle();
      } else {
        newickStringName = "Tree Block: " + TB.getTitle();
      }

      for (PhyloTree aTree : TB.getTreeList()) {
        treeMap.put(getMapKey(aTree), aTree.getId() + separator + aTree.getNewickString()
          + separator + "T");
        phylowsMap.put(getMapKey(aTree), aTree.getTreebaseIDString().getNamespacedGUID().toString());
        if ( defaultNewick.equals("") ) {
          defaultNewick = aTree.getNewickString();
        }
        treeList.add(aTree);
      }         
      // XXX ok, so this mess started when we somehow combined phylowidget for searching
      // with phylowidget for submission (why???) -- rvosa
      if ( TB.getTreeListIterator().hasNext() ) {
        Study study = TB.getTreeListIterator().next().getStudy();
        if ( study != null && study.isPublished() ) {
          pRequest.getSession().setAttribute("treeBlockID", TB.getId());
          if ( TB.getTreeListIterator().hasNext() ) {
            pRequest.getSession().setAttribute("studyID", study.getId());
          }
        }
      }
    }
View Full Code Here
178
179
180
181
182
183
184
185
186
187
188
189
        }     
      }
      else if ( dataType.equals("TreeBlocks") ) {
        for ( int i = 0; i < ids.length; i++ ) {
          if ( ! TreebaseUtil.isEmpty(ids[i]) ) {
            TreeBlock treeBlock = getPhyloTreeService().findTreeBlockByID(Long.parseLong(ids[i]));
            for ( PhyloTree phyloTree : treeBlock.getTreeList() ) {
              AnalyzedTree analyzedTree = new AnalyzedTree();
              analyzedTree.setInput(input);
              analyzedTree.setTree(phyloTree);
              analysisStep.addAnalyzedData(analyzedTree);
              getAnalysisStepService().update(analysisStep);           
View Full Code Here
TOP

Related Classes of org.cipres.treebase.domain.tree.TreeBlock

  • org.cipres.treebase.auxdata.CommitStudy
  • org.cipres.treebase.dao.tree.PhyloTreeDAO
  • org.cipres.treebase.dao.tree.PhyloTreeDAOTest
  • org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter
  • org.cipres.treebase.domain.nexus.nexml.NexmlConverter
  • org.cipres.treebase.domain.nexus.nexml.NexmlTreeBlockReader
  • org.cipres.treebase.domain.nexus.NexmlSerializationTest
  • org.cipres.treebase.domain.study.Study
  • org.cipres.treebase.domain.taxon.TaxonLabelSet
  • org.cipres.treebase.util.RepatriateData
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.